CAP - Catabolite gene Activating Protein (1BER)

Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI)

GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)

Virtual reality with YASARA in Linux and Windows

Since the very beginning, interactive molecular modeling has heavily benefited from a stereoscopic three-dimensional view, obtained mostly with the help of shutter glasses. While co-evolution with the video gaming industry brought 3D glasses for everyone during the 2010s, the shift to the more captivating virtual reality headsets has left modelers stranded without supply. Walking around and waving arms in a virtual world is great, but too tiring for hours of hard modeling work.

Since April 2023, YASARA combines the best of both worlds. Using a popular VR headset like Vive, Index, or Quest 2, the user sits in front of the normal screen, which is beamed into the virtual reality together with keyboard, mouse and chair using the headset’s cameras and an extra tracker attached to the seat-back. Compared to shutter glasses, this yields an equally relaxing, but much more immersive workplace, with the additional possibilities to take molecules into one's hands, stand up, and walk or teleport through the models.

Just watch the video on the right to get an overview and introduction to VR with YASARA. If you want to virtualize yourself, you need YASARA Model or a higher YASARA stage. Please see the detailed setup guide in the YASARA user manual, which lists the pros and cons of each headset supported. The easiest and cheapest way to get in touch with VR is the Meta Quest 2, while the best solution is the Vive Pro shown in the video, with an extra Vive tracker 3.0 to virtualize your chair. Since the Vive Pro is already in short supply, please act quickly.

Additional information:

Our ranking of VR headsets with hints where to buy those that are in short supply.
The PetWorld database with a growing collection of mega- and gigastructures.
How YASARA's Vulkan graphics engine[1] brings giant structures to VR.
How you can build giant structures yourself and get YASARA for free in return.
How to use virtual reality with Android smartphones
An extensive guide on how to choose the right headset and install the VR system is in the user manual of all YASARA stages (can be found in the Help menu) at Essentials > Running YASARA in special environments > Running YASARA in virtual reality mode on PCs.
If you encounter any problems with VR, check the user manual at Troubleshooting > Virtual reality doesn't work as expected.

R E F E R E N C E S

[1] Assembly of biomolecular gigastructures and visualization with the Vulkan graphics API
Ozvoldik K, Stockner T, Rammner B, and Krieger E (2021). Journal of Chemical Information and Modeling 61, 5293-5303

Figure 1: The video above shows how to get started with virtual reality in YASARA. It proves that the concept is so simple and user-friendly, that even 11-year old kids can work with it. If your browser fails to play the video, here is a YouTube link with worse quality.

Figure 2: These are the VR headsets we bought and tested extensively in Linux and Windows. They are thus officially supported, other headsets may work with limitations or not at all.

Figure 3: Overview of a VR setup with YASARA. Click the image for a larger version. Outside-in tracking with base stations (Vive, Index) and inside-out tracking without base stations (Quest 2) are both supported. Attaching a tracker to the chair to create a digital twin is currently only possible with outside-in tracking (Vive Tracker 3.0), but alternatives are in development.